Cadmium in PDB 5azg: Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide
Protein crystallography data
The structure of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide, PDB code: 5azg
was solved by
Y.Watanabe,
Y.Fujioka,
N.N.Noda,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
55.75 /
1.81
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.684,
80.116,
111.500,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.2 /
24.6
|
Cadmium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
14;
Binding sites:
The binding sites of Cadmium atom in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide
(pdb code 5azg). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 14 binding sites of Cadmium where determined in the
Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide, PDB code: 5azg:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Cadmium binding site 1 out
of 14 in 5azg
Go back to
Cadmium Binding Sites List in 5azg
Cadmium binding site 1 out
of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd201
b:37.5
occ:1.00
|
NE2
|
A:HIS0
|
2.3
|
36.6
|
1.0
|
O
|
A:GLY116
|
2.5
|
42.6
|
1.0
|
OXT
|
A:GLY116
|
2.5
|
40.1
|
1.0
|
C
|
A:GLY116
|
2.9
|
42.5
|
1.0
|
CE1
|
A:HIS0
|
3.2
|
36.9
|
1.0
|
CD2
|
A:HIS0
|
3.3
|
37.1
|
1.0
|
ND1
|
A:HIS0
|
4.4
|
36.0
|
1.0
|
CA
|
A:GLY116
|
4.4
|
43.7
|
1.0
|
CG
|
A:HIS0
|
4.4
|
35.8
|
1.0
|
O
|
A:HOH317
|
4.8
|
37.7
|
1.0
|
|
Cadmium binding site 2 out
of 14 in 5azg
Go back to
Cadmium Binding Sites List in 5azg
Cadmium binding site 2 out
of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd202
b:70.4
occ:1.00
|
OE2
|
A:GLU17
|
2.5
|
45.3
|
1.0
|
OE1
|
A:GLU17
|
2.8
|
47.5
|
1.0
|
CD
|
A:GLU17
|
3.0
|
44.2
|
1.0
|
O
|
C:HOH404
|
3.8
|
42.9
|
1.0
|
NZ
|
A:LYS48
|
4.3
|
45.8
|
1.0
|
CG
|
A:GLU17
|
4.5
|
41.0
|
1.0
|
O
|
C:HOH405
|
4.5
|
63.3
|
1.0
|
CE1
|
C:PHE358
|
4.6
|
41.9
|
1.0
|
OD1
|
C:ASP357
|
5.0
|
57.9
|
1.0
|
|
Cadmium binding site 3 out
of 14 in 5azg
Go back to
Cadmium Binding Sites List in 5azg
Cadmium binding site 3 out
of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd203
b:51.1
occ:1.00
|
O
|
A:HOH301
|
1.7
|
34.7
|
1.0
|
OD1
|
A:ASP45
|
2.4
|
50.8
|
1.0
|
OD2
|
A:ASP45
|
2.6
|
49.4
|
1.0
|
CG
|
A:ASP45
|
2.8
|
49.9
|
1.0
|
CB
|
A:ASP45
|
4.3
|
48.0
|
1.0
|
O
|
A:ASP45
|
4.4
|
47.2
|
1.0
|
NZ
|
A:LYS46
|
4.9
|
56.2
|
1.0
|
CE
|
A:LYS46
|
4.9
|
54.6
|
1.0
|
C
|
A:ASP45
|
4.9
|
46.3
|
1.0
|
CA
|
A:ASP45
|
5.0
|
47.2
|
1.0
|
|
Cadmium binding site 4 out
of 14 in 5azg
Go back to
Cadmium Binding Sites List in 5azg
Cadmium binding site 4 out
of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd204
b:37.6
occ:1.00
|
O
|
A:HOH328
|
2.2
|
47.1
|
1.0
|
OD2
|
A:ASP97
|
2.3
|
31.1
|
1.0
|
OD1
|
A:ASP97
|
2.7
|
32.5
|
1.0
|
CG
|
A:ASP97
|
2.8
|
31.6
|
1.0
|
OE1
|
A:GLN96
|
3.9
|
37.8
|
1.0
|
CB
|
A:ASP97
|
4.3
|
29.9
|
1.0
|
O
|
A:HOH310
|
4.6
|
34.9
|
1.0
|
O
|
A:HOH336
|
4.7
|
46.6
|
1.0
|
O
|
A:GLN93
|
4.9
|
28.5
|
1.0
|
|
Cadmium binding site 5 out
of 14 in 5azg
Go back to
Cadmium Binding Sites List in 5azg
Cadmium binding site 5 out
of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd205
b:40.5
occ:1.00
|
O
|
A:HOH336
|
2.1
|
46.6
|
1.0
|
O
|
A:HOH338
|
2.2
|
73.8
|
1.0
|
O
|
A:HOH341
|
2.4
|
39.5
|
1.0
|
NE2
|
A:HIS98
|
2.4
|
30.6
|
1.0
|
O
|
A:HOH310
|
2.4
|
34.9
|
1.0
|
O
|
A:HOH339
|
2.7
|
48.4
|
1.0
|
CD2
|
A:HIS98
|
3.3
|
30.3
|
1.0
|
CE1
|
A:HIS98
|
3.4
|
31.8
|
1.0
|
OD2
|
A:ASP97
|
4.1
|
31.1
|
1.0
|
O
|
A:HOH313
|
4.2
|
50.5
|
1.0
|
CB
|
A:ASP97
|
4.5
|
29.9
|
1.0
|
CG
|
A:HIS98
|
4.5
|
29.0
|
1.0
|
ND1
|
A:HIS98
|
4.5
|
31.0
|
1.0
|
CG
|
A:ASP97
|
4.8
|
31.6
|
1.0
|
|
Cadmium binding site 6 out
of 14 in 5azg
Go back to
Cadmium Binding Sites List in 5azg
Cadmium binding site 6 out
of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd206
b:39.0
occ:1.00
|
O
|
B:HOH335
|
2.0
|
43.3
|
1.0
|
O
|
B:HOH327
|
2.2
|
45.0
|
1.0
|
OD2
|
A:ASP27
|
2.3
|
38.5
|
1.0
|
OD1
|
B:ASP54
|
2.3
|
35.1
|
1.0
|
OD2
|
B:ASP54
|
2.4
|
39.8
|
1.0
|
OD1
|
A:ASP27
|
2.4
|
37.1
|
1.0
|
O
|
B:HOH344
|
2.4
|
45.5
|
1.0
|
CG
|
A:ASP27
|
2.6
|
37.4
|
1.0
|
CG
|
B:ASP54
|
2.7
|
36.9
|
1.0
|
CB
|
A:ASP27
|
4.2
|
36.0
|
1.0
|
CB
|
B:ASP54
|
4.2
|
36.5
|
1.0
|
O
|
B:HOH336
|
4.2
|
40.1
|
1.0
|
O
|
B:HOH337
|
4.3
|
43.5
|
1.0
|
CB
|
B:PRO52
|
4.6
|
29.4
|
1.0
|
CA
|
A:ASP27
|
5.0
|
34.0
|
1.0
|
N
|
B:ASP54
|
5.0
|
34.6
|
1.0
|
N
|
A:ASP27
|
5.0
|
34.3
|
1.0
|
CA
|
B:ASP54
|
5.0
|
35.0
|
1.0
|
|
Cadmium binding site 7 out
of 14 in 5azg
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Cadmium Binding Sites List in 5azg
Cadmium binding site 7 out
of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd207
b:51.9
occ:1.00
|
O
|
A:HOH303
|
2.4
|
39.8
|
1.0
|
O
|
B:HOH337
|
2.5
|
43.5
|
1.0
|
OD1
|
A:ASP27
|
4.0
|
37.1
|
1.0
|
O
|
B:HOH335
|
4.2
|
43.3
|
1.0
|
OD2
|
B:ASP27
|
4.3
|
40.8
|
1.0
|
O
|
B:HOH344
|
4.4
|
45.5
|
1.0
|
O
|
B:HOH343
|
4.7
|
50.2
|
1.0
|
OG
|
A:SER53
|
4.7
|
30.9
|
1.0
|
|
Cadmium binding site 8 out
of 14 in 5azg
Go back to
Cadmium Binding Sites List in 5azg
Cadmium binding site 8 out
of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd208
b:42.1
occ:1.00
|
O
|
B:HOH331
|
2.0
|
52.7
|
1.0
|
OD2
|
B:ASP27
|
2.1
|
40.8
|
1.0
|
OD2
|
A:ASP54
|
2.4
|
34.7
|
1.0
|
O
|
B:HOH343
|
2.4
|
50.2
|
1.0
|
OD1
|
A:ASP54
|
2.6
|
37.5
|
1.0
|
CG
|
A:ASP54
|
2.8
|
34.7
|
1.0
|
CG
|
B:ASP27
|
2.9
|
36.6
|
1.0
|
OD1
|
B:ASP27
|
2.9
|
38.4
|
1.0
|
CB
|
B:ASP27
|
4.3
|
34.6
|
1.0
|
CB
|
A:ASP54
|
4.3
|
33.4
|
1.0
|
O
|
A:HOH303
|
4.3
|
39.8
|
1.0
|
OG
|
A:SER53
|
4.4
|
30.9
|
1.0
|
O
|
B:HOH337
|
4.6
|
43.5
|
1.0
|
NE
|
B:ARG28
|
4.7
|
30.9
|
1.0
|
|
Cadmium binding site 9 out
of 14 in 5azg
Go back to
Cadmium Binding Sites List in 5azg
Cadmium binding site 9 out
of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 9 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd201
b:33.7
occ:1.00
|
O
|
B:HOH313
|
2.2
|
63.4
|
1.0
|
NE2
|
B:HIS0
|
2.2
|
30.8
|
1.0
|
O
|
B:GLY116
|
2.3
|
53.9
|
1.0
|
OXT
|
B:GLY116
|
2.5
|
48.4
|
1.0
|
C
|
B:GLY116
|
2.8
|
50.9
|
1.0
|
O
|
B:HOH304
|
3.1
|
41.1
|
1.0
|
CE1
|
B:HIS0
|
3.2
|
31.0
|
1.0
|
CD2
|
B:HIS0
|
3.2
|
31.9
|
1.0
|
CA
|
B:GLY116
|
4.3
|
49.8
|
1.0
|
ND1
|
B:HIS0
|
4.3
|
30.5
|
1.0
|
CG
|
B:HIS0
|
4.4
|
31.5
|
1.0
|
|
Cadmium binding site 10 out
of 14 in 5azg
Go back to
Cadmium Binding Sites List in 5azg
Cadmium binding site 10 out
of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 10 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd202
b:33.3
occ:1.00
|
O
|
B:HOH340
|
2.2
|
41.0
|
1.0
|
NE2
|
B:HIS99
|
2.3
|
28.0
|
1.0
|
O
|
B:HOH347
|
2.6
|
39.8
|
1.0
|
CE1
|
B:HIS99
|
3.2
|
29.6
|
1.0
|
CD2
|
B:HIS99
|
3.5
|
28.6
|
1.0
|
O
|
B:HOH314
|
4.3
|
40.5
|
1.0
|
ND1
|
B:HIS99
|
4.4
|
29.2
|
1.0
|
CG
|
B:HIS99
|
4.5
|
28.3
|
1.0
|
O
|
B:HOH315
|
5.0
|
49.6
|
1.0
|
|
Reference:
F.Wu,
Y.Watanabe,
X.Y.Guo,
X.Qi,
P.Wang,
H.Y.Zhao,
Z.Wang,
Y.Fujioka,
H.Zhang,
J.Q.Ren,
T.C.Fang,
Y.X.Shen,
W.Feng,
J.J.Hu,
N.N.Noda,
H.Zhang.
Structural Basis of the Differential Function of the Two C. Elegans ATG8 Homologs, Lgg-1 and Lgg-2, in Autophagy Mol.Cell V. 60 914 2015.
ISSN: ISSN 1097-2765
DOI: 10.1016/J.MOLCEL.2015.11.019
Page generated: Fri Jul 19 18:12:00 2024
|